diff --git a/docs/_posts/SKocer/2023-04-10-medication_resolver_pipeline_en.md b/docs/_posts/SKocer/2023-04-10-medication_resolver_pipeline_en.md new file mode 100644 index 0000000000..3a126dcb05 --- /dev/null +++ b/docs/_posts/SKocer/2023-04-10-medication_resolver_pipeline_en.md @@ -0,0 +1,105 @@ +--- +layout: model +title: Pipeline to Resolve Medication Codes +author: John Snow Labs +name: medication_resolver_pipeline +date: 2023-04-10 +tags: [resolver, snomed, umls, rxnorm, ndc, ade, en, licensed, pipeline] +task: Entity Resolution +language: en +edition: Healthcare NLP 4.3.2 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +A pretrained resolver pipeline to extract medications and resolve their adverse reactions (ADE), RxNorm, UMLS, NDC, SNOMED CT codes, and action/treatments in clinical text. + +Action/treatments are available for branded medication, and SNOMED codes are available for non-branded medication. + +This pipeline can be used as Lightpipeline (with `annotate/fullAnnotate`). You can use `medication_resolver_transform_pipeline` for Spark transform. + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/medication_resolver_pipeline_en_4.3.2_3.0_1681151954032.zip){:.button.button-orange} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/medication_resolver_pipeline_en_4.3.2_3.0_1681151954032.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} +```python +from sparknlp.pretrained import PretrainedPipeline + +med_resolver_pipeline = PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models") + +text = """The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""" + +result = med_resolver_pipeline.fullAnnotate(text) +``` +```scala +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val med_resolver_pipeline = new PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models") + +val result = med_resolver_pipeline.fullAnnotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""") +``` +
+ +## Results + +```bash +| | chunks | entities | ADE | RxNorm | Action | Treatment | UMLS | SNOMED_CT | NDC_Product | NDC_Package | +|---:|:-----------------------------|:-----------|:----------------------------|---------:|:---------------------------|:-------------------------------------------|:---------|:------------|:--------------|:--------------| +| 0 | Amlodopine Vallarta 10-320mg | DRUG | Gynaecomastia | 722131 | NONE | NONE | C1949334 | 425838008 | 00093-7693 | 00093-7693-56 | +| 1 | Eviplera | DRUG | Anxiety | 217010 | Inhibitory Bone Resorption | Osteoporosis | C0720318 | NONE | NONE | NONE | +| 2 | Lescol 40 MG | DRUG | NONE | 103919 | Hypocholesterolemic | Heterozygous Familial Hypercholesterolemia | C0353573 | NONE | 00078-0234 | 00078-0234-05 | +| 3 | Everolimus 1.5 mg tablet | DRUG | Acute myocardial infarction | 2056895 | NONE | NONE | C4723581 | NONE | 00054-0604 | 00054-0604-21 | +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|medication_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 4.3.2+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|3.2 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetectorDLModel +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverterInternalModel +- TextMatcherModel +- ChunkMergeModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger +- ResolverMerger +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- Finisher \ No newline at end of file diff --git a/docs/_posts/SKocer/2023-04-11-medication_resolver_transform_pipeline_en.md b/docs/_posts/SKocer/2023-04-11-medication_resolver_transform_pipeline_en.md new file mode 100644 index 0000000000..b5781440fc --- /dev/null +++ b/docs/_posts/SKocer/2023-04-11-medication_resolver_transform_pipeline_en.md @@ -0,0 +1,111 @@ +--- +layout: model +title: Pipeline to Resolve Medication Codes(Transform) +author: John Snow Labs +name: medication_resolver_transform_pipeline +date: 2023-04-11 +tags: [resolver, rxnorm, ndc, snomed, umls, ade, pipeline, en, licensed] +task: Entity Resolution +language: en +edition: Healthcare NLP 4.3.2 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +A pretrained resolver pipeline to extract medications and resolve their adverse reactions (ADE), RxNorm, UMLS, NDC, SNOMED CT codes, and action/treatments in clinical text. + +Action/treatments are available for branded medication, and SNOMED codes are available for non-branded medication. + +This pipeline can be used with Spark transform. You can use `medication_resolver_pipeline` as Lightpipeline (with `annotate/fullAnnotate`). + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/medication_resolver_transform_pipeline_en_4.3.2_3.0_1681190723377.zip){:.button.button-orange} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/medication_resolver_transform_pipeline_en_4.3.2_3.0_1681190723377.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} +```python +from sparknlp.pretrained import PretrainedPipeline + +medication_resolver_pipeline = PretrainedPipeline("medication_resolver_transform_pipeline", "en", "clinical/models") + +text = """The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""" + +data = spark.createDataFrame([[text]]).toDF("text") + +result = medication_resolver_pipeline.transform(data) +``` +```scala +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val medication_resolver_pipeline = new PretrainedPipeline("medication_resolver_transform_pipeline", "en", "clinical/models") + +val data = Seq("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""").toDS.toDF("text") + +val result = medication_resolver_pipeline.fit(data).transform(data) +``` +
+ +## Results + +```bash +| chunk | ner_label | ADE | RxNorm | Action | Treatment | UMLS | SNOMED_CT | NDC_Product | NDC_Package | +|:-----------------------------|:------------|:----------------------------|---------:|:---------------------------|:-------------------------------------------|:---------|:------------|:--------------|:--------------| +| Amlodopine Vallarta 10-320mg | DRUG | Gynaecomastia | 722131 | NONE | NONE | C1949334 | 425838008 | 00093-7693 | 00093-7693-56 | +| Eviplera | DRUG | Anxiety | 217010 | Inhibitory Bone Resorption | Osteoporosis | C0720318 | NONE | NONE | NONE | +| Lescol 40 MG | DRUG | NONE | 103919 | Hypocholesterolemic | Heterozygous Familial Hypercholesterolemia | C0353573 | NONE | 00078-0234 | 00078-0234-05 | +| Everolimus 1.5 mg tablet | DRUG | Acute myocardial infarction | 2056895 | NONE | NONE | C4723581 | NONE | 00054-0604 | 00054-0604-21 | +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|medication_resolver_transform_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 4.3.2+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|3.2 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetectorDLModel +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverterInternalModel +- TextMatcherModel +- ChunkMergeModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger +- Doc2Chunk +- ResolverMerger +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- Doc2Chunk +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- Finisher \ No newline at end of file